CPGs reads sumary

## 129 observations with both PAH31 and CPG sites data from 104 unique subjects.
##    cg05575921       cg21566642       cg01940273       cg21161138    
##  Min.   :0.6293   Min.   :0.2730   Min.   :0.4667   Min.   :0.5821  
##  1st Qu.:0.8116   1st Qu.:0.3904   1st Qu.:0.5521   1st Qu.:0.6856  
##  Median :0.8458   Median :0.4258   Median :0.5765   Median :0.7076  
##  Mean   :0.8391   Mean   :0.4220   Mean   :0.5775   Mean   :0.7047  
##  3rd Qu.:0.8840   3rd Qu.:0.4603   3rd Qu.:0.6064   3rd Qu.:0.7326  
##  Max.   :0.9173   Max.   :0.5670   Max.   :0.6906   Max.   :0.7780  
##    cg03329539       cg03636183       cg09935388       cg19859270    
##  Min.   :0.2759   Min.   :0.4846   Min.   :0.5959   Min.   :0.8477  
##  1st Qu.:0.3394   1st Qu.:0.6420   1st Qu.:0.7794   1st Qu.:0.9078  
##  Median :0.3625   Median :0.6730   Median :0.8085   Median :0.9157  
##  Mean   :0.3657   Mean   :0.6678   Mean   :0.8013   Mean   :0.9144  
##  3rd Qu.:0.3885   3rd Qu.:0.6950   3rd Qu.:0.8371   3rd Qu.:0.9242  
##  Max.   :0.4879   Max.   :0.7495   Max.   :0.8825   Max.   :0.9406  
##    cg09198866       cg00811020        cg01411366    
##  Min.   :0.8682   Min.   :0.08161   Min.   :0.2108  
##  1st Qu.:0.8999   1st Qu.:0.14166   1st Qu.:0.3945  
##  Median :0.9113   Median :0.16929   Median :0.4324  
##  Mean   :0.9115   Mean   :0.16888   Mean   :0.4303  
##  3rd Qu.:0.9221   3rd Qu.:0.19690   3rd Qu.:0.4654  
##  Max.   :0.9528   Max.   :0.34424   Max.   :0.6284

PAH31 ~ CPG site

not adjusted for confounders

adjusted for confounders

current 5mc ~ CPG site

not adjusted for confounders

cummulative 5mc ~ CPG site

not adjusted for confounders

childhood 5mc ~ CPG site

not adjusted for confounders

CPG site ~ Current fuel type

GEE (with confounders, Smokeless ref)

The numbers of observations with each current fuel type:

## 
##          Smokeles             Smoky Wood_and_or_Plant 
##                18               100                14

In this section, we perform the generalized estimating equations (GEE) to evaluate the associations between current fuel type and each CpG site reads with the formula: \[ \begin{aligned} Y = & \beta_0 + \beta_1 * I(\text{Smoky}) + \beta_2 * I(\text{Wood_and_or_Plant}) \\ & + \beta_3 * county + \beta_4 * BMI + \beta_5 * ses + \beta_6 * edu + \epsilon \end{aligned} \]

Results:

## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."

## The estimated average EAA differences of Smoky fuel type to Smokeless fuel yupes:
##            coefficient    std ci_lower ci_upper    p_val sig_level
## cg05575921     -0.0453 0.0103  -0.0655  -0.0252 0.000010  <= 0.001
## cg21566642     -0.0244 0.0148  -0.0535   0.0047 0.100600    > 0.05
## cg01940273     -0.0262 0.0100  -0.0459  -0.0066 0.008778   <= 0.01
## cg21161138     -0.0204 0.0090  -0.0380  -0.0027 0.023707   <= 0.05
## cg03329539     -0.0017 0.0081  -0.0176   0.0141 0.830765    > 0.05
## cg03636183     -0.0456 0.0102  -0.0655  -0.0256 0.000007  <= 0.001
## cg09935388     -0.0039 0.0134  -0.0301   0.0223 0.771875    > 0.05
## cg19859270     -0.0014 0.0049  -0.0110   0.0082 0.772623    > 0.05
## cg09198866      0.0015 0.0051  -0.0084   0.0115 0.762496    > 0.05
## cg00811020      0.0051 0.0096  -0.0138   0.0240 0.598073    > 0.05
## cg01411366     -0.0055 0.0148  -0.0345   0.0235 0.711272    > 0.05
## The estimated average EAA differences of Wood and/or Plant fuel type to Smokeless fuel yupes:
##            coefficient    std ci_lower ci_upper    p_val sig_level
## cg05575921     -0.0572 0.0134  -0.0835  -0.0309 0.000020  <= 0.001
## cg21566642     -0.0316 0.0204  -0.0716   0.0084 0.121770    > 0.05
## cg01940273     -0.0283 0.0131  -0.0540  -0.0027 0.030076   <= 0.05
## cg21161138     -0.0067 0.0118  -0.0298   0.0163 0.568266    > 0.05
## cg03329539     -0.0060 0.0114  -0.0284   0.0163 0.596737    > 0.05
## cg03636183     -0.0388 0.0125  -0.0633  -0.0144 0.001843   <= 0.01
## cg09935388     -0.0056 0.0128  -0.0308   0.0196 0.662370    > 0.05
## cg19859270     -0.0053 0.0051  -0.0153   0.0048 0.305401    > 0.05
## cg09198866     -0.0029 0.0058  -0.0143   0.0085 0.617203    > 0.05
## cg00811020     -0.0075 0.0152  -0.0373   0.0222 0.620596    > 0.05
## cg01411366      0.0288 0.0210  -0.0124   0.0699 0.170474    > 0.05

GEE (without confounders, Smokeless ref)

The numbers of observations with each current fuel type:

## 
##          Smokeles             Smoky Wood_and_or_Plant 
##                18               100                14

In this section, we perform the generalized estimating equations (GEE) to evaluate the associations between current fuel type and each CpG site reads with the formula: \[ \begin{aligned} Y = & \beta_0 + \beta_1 * I(\text{Smoky}) + \beta_2 * I(\text{Wood_and_or_Plant}) \\ & + \epsilon \end{aligned} \]

Results:

## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."

## The estimated average EAA differences of Smoky fuel type to Smokeless fuel yupes:
##            coefficient    std ci_lower ci_upper    p_val sig_level
## cg05575921     -0.0421 0.0075  -0.0568  -0.0273 0.000000  <= 0.001
## cg21566642     -0.0108 0.0133  -0.0368   0.0153 0.417026    > 0.05
## cg01940273     -0.0135 0.0097  -0.0326   0.0056 0.166367    > 0.05
## cg21161138     -0.0153 0.0082  -0.0313   0.0006 0.060034    > 0.05
## cg03329539      0.0039 0.0077  -0.0113   0.0190 0.616536    > 0.05
## cg03636183     -0.0340 0.0080  -0.0496  -0.0184 0.000020  <= 0.001
## cg09935388     -0.0052 0.0121  -0.0290   0.0186 0.668365    > 0.05
## cg19859270     -0.0006 0.0049  -0.0102   0.0089 0.895578    > 0.05
## cg09198866      0.0013 0.0048  -0.0081   0.0107 0.784650    > 0.05
## cg00811020     -0.0039 0.0081  -0.0198   0.0119 0.625883    > 0.05
## cg01411366     -0.0026 0.0143  -0.0306   0.0254 0.855045    > 0.05
## The estimated average EAA differences of Wood and/or Plant fuel type to Smokeless fuel yupes:
##            coefficient    std ci_lower ci_upper    p_val sig_level
## cg05575921     -0.0586 0.0143  -0.0866  -0.0307 0.000040  <= 0.001
## cg21566642     -0.0262 0.0214  -0.0682   0.0159 0.222283    > 0.05
## cg01940273     -0.0221 0.0137  -0.0490   0.0048 0.107285    > 0.05
## cg21161138     -0.0026 0.0112  -0.0245   0.0194 0.818688    > 0.05
## cg03329539     -0.0023 0.0117  -0.0253   0.0208 0.847698    > 0.05
## cg03636183     -0.0339 0.0124  -0.0582  -0.0096 0.006268   <= 0.01
## cg09935388     -0.0047 0.0121  -0.0285   0.0190 0.696191    > 0.05
## cg19859270     -0.0050 0.0055  -0.0158   0.0058 0.363770    > 0.05
## cg09198866     -0.0027 0.0058  -0.0141   0.0086 0.638459    > 0.05
## cg00811020     -0.0117 0.0143  -0.0398   0.0163 0.411798    > 0.05
## cg01411366      0.0264 0.0214  -0.0155   0.0683 0.217460    > 0.05